American Floyd Landis finished fourth and reclaimed the overall lead in cycling's most prestigious event.
Schleck completed Tuesday's 187-kilometer mountain stage from Gap to L'Alpe-d'Huez in a time of 4 hours, 52 minutes and 22 seconds, beating Italy's Damiano Cunego by 11 seconds.
Stefano Garzelli of Italy was third, 1:10 behind, while Landis and Germany's Andreas Kloden rounded out the top five with the same time.
Landis, who held the overall lead for two days last week, started the day 1:29 behind overall leader Oscar Pereiro of Spain. Pereiro was among a group behind Landis and could only manage a 14th-place finish on Tuesday, 2:49 off the lead pace. He is now second overall, 10 seconds behind Landis.
Ray Liotta sues skin care company over use of likeness
Boston schools pull out free condoms over wrapping complaints